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1 import argparse
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2 import csv
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3 import logging
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4 import os
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5 import sys
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6 from collections import defaultdict
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7 from collections import namedtuple
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8
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9 from Bio import SeqIO
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10 from Bio.Alphabet import generic_dna
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11 from Bio.Seq import Seq
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12 from Bio.SeqRecord import SeqRecord
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13
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14
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15 def sniff_format(file_path):
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16 """
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17 Try to guess the file format (fastq/fasta) by looking at the first character of the first line.
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18 Should be '@' for fastq and '>' for fasta.
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19 """
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3
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20 with open(file_path, 'r') as file_handle:
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0
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21 for line in file_handle:
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22 if line.startswith("@"):
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23 return "fastq"
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24 if line.startswith(">"):
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25 return "fasta"
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26 break
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27 return None
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28
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3
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29
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0
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30 def search_barcode_in_first_half(sequence, barcode):
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31 if type(sequence) is Seq:
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4
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32 sequence = str(sequence).lower()
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33 elif type(sequence) is SeqRecord:
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4
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34 sequence = str(sequence.seq).lower()
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35 return sequence.find(barcode, 0, int(len(sequence) / 2))
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36
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37
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38 def search_barcode_in_second_half(sequence, barcode):
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39 if type(sequence) is Seq:
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4
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40 sequence = str(sequence).lower()
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41 elif type(sequence) is SeqRecord:
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4
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42 sequence = str(sequence.seq).lower()
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43 return sequence.find(barcode, int(len(sequence) / 2))
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44
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45
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46 def search_barcodes_in_sequence(barcode_datas, sequence):
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47 for barcode_data in barcode_datas:
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48 barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode)
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49 if barcode_search_position != -1:
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50 return barcode_search_position, barcode_data, False
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51 barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode_reverse)
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52 if barcode_search_position != -1:
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53 return barcode_search_position, barcode_data, True
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54
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55 barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode_reverse)
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56 if barcode_search_position != -1:
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57 return barcode_search_position, barcode_data, True
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58
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59 barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode)
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60 if barcode_search_position != -1:
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61 return barcode_search_position, barcode_data, False
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62
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63 return -1, None, None
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64
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65
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66 def main():
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67 parser = argparse.ArgumentParser()
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68 parser.add_argument("-i", "--input", help="The input file", required=True)
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69 parser.add_argument("-f", "--format", help="The format of the input file (fastq/fasta)", default="auto", choices=["fasta", "fastq", "auto"])
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70 parser.add_argument("-o", "--output-dir", help="The output dir", required=True)
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71 parser.add_argument("-m", "--mapping-file", help="A tab seperated file containing two columns, ID and barcode (no header)", required=True)
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72
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73 args = parser.parse_args()
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74
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75 input_file_path = args.input
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76 basename_input_file_path = os.path.basename(input_file_path)
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77 input_basename_no_ext, input_extension = os.path.splitext(basename_input_file_path)
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78
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79 input_format = args.format
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80
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81 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
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82
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83 if input_format == "auto":
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84 if input_extension in [".fasta", ".fa"]:
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85 input_format = "fasta"
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86 elif input_extension in [".fastq", ".fq"]:
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87 input_format = "fastq"
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88 else:
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89 logging.info("Can't auto detect input format based on extension: {0}".format(input_extension))
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90 logging.info("Sniffing format...")
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91 input_format = sniff_format(input_file_path)
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92 if not input_format:
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93 logging.error("Can't auto detect input format")
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94 sys.exit(1)
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95 logging.info("Sniffed '{0}' as format.".format(input_format))
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96
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97 output_dir = args.output_dir
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98 if not os.path.exists(output_dir):
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99 os.makedirs(output_dir)
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100
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101 with open(args.mapping_file, newline="") as handle:
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102 ID_barcode_mapping = list(csv.DictReader(handle, fieldnames=['ID', 'barcode'], delimiter="\t"))
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103
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104 logging.info("Input: {0}".format(input_file_path))
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105 logging.info("Format: {0}".format(input_format))
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106 logging.info("Output: {0}".format(output_dir))
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107 logging.info("Mapping: {0} ({1} mappings)".format(args.mapping_file, len(ID_barcode_mapping)))
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108
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109 BarcodeData = namedtuple("BarcodeData", [
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110 "ID",
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111 "barcode",
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112 "barcode_reverse",
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113 "output_file_path",
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114 "output_file_handle"
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115 ])
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116
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117 barcode_data_dict = defaultdict(list)
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118 ID_file_handle_dict = {}
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119
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120 for ID_barcode in ID_barcode_mapping:
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121 ID = ID_barcode["ID"]
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122 barcode = ID_barcode["barcode"]
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123
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124 logging.info("{0}:\t\t{1}".format(ID, barcode))
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125
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126 output_file_path = os.path.join(
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127 output_dir,
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128 "{0}.{1}".format(ID, input_format)
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129 )
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130
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131 if ID not in ID_file_handle_dict:
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132 ID_file_handle = open(output_file_path, 'w')
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133 ID_file_handle_dict[ID] = ID_file_handle
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134
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135 ID_file_handle = ID_file_handle_dict[ID]
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136
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137 barcode_data_dict[ID] += [BarcodeData(
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138 ID=ID,
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139 barcode=barcode.lower(),
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140 barcode_reverse=str(Seq(barcode, generic_dna).reverse_complement()).lower(),
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141 output_file_path=output_file_path,
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142 output_file_handle=ID_file_handle
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143 )]
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144
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145 discarded_output_file_path = os.path.join(
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146 output_dir,
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147 "{0}.{1}".format("discarded", input_format)
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148 )
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149
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150 total_sequences = 0
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151 sequences_assigned_by_id = defaultdict(int)
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152
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3
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153 with open(input_file_path, 'r') as input_file_handle, open(discarded_output_file_path, 'w') as discarded_output_handle:
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154 for record in SeqIO.parse(input_file_handle, input_format):
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155 total_sequences += 1
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156 for ID, barcode_datas in barcode_data_dict.items():
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157 barcode_position, barcode_data, reverse = search_barcodes_in_sequence(barcode_datas, record)
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158 if barcode_position == -1:
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159 continue
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160 barcode = barcode_data.barcode if not reverse else barcode_data.barcode_reverse
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161 sequences_assigned_by_id[barcode_data.ID] += 1
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162 logging.debug(str(record.seq))
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163 logging.debug(" " * barcode_position + barcode)
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164 SeqIO.write(record, ID_file_handle_dict[ID], input_format)
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165 break
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166 else: # no match # TODO fuzzy match ?
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167 SeqIO.write(record, discarded_output_handle, input_format)
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168 if total_sequences % 10000 == 0:
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169 assigned_sequences = sum(sequences_assigned_by_id.values())
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170 logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
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171 total_sequences,
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172 assigned_sequences,
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173 round(assigned_sequences / total_sequences * 100)
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174 ))
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175
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176 for file_handle in ID_file_handle_dict.values():
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177 file_handle.close()
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178
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179 assigned_sequences = sum(sequences_assigned_by_id.values())
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180 logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
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181 total_sequences,
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182 assigned_sequences,
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183 round(assigned_sequences / total_sequences * 100)
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184 ))
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185
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186
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187 if __name__ == "__main__":
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188 main()
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189
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